Walking down a set of rusting stairs, under a crumbling ceiling, along a debris-strewn platform and past a ruined control room, Wynton Habersham finally arrived at the most devastated part of the South Ferry subway station: A room full of electrical equipment, corroding from the effects of almost 15 million gallons of salt water that flooded it during Superstorm Sandy.

“It is completely nonfunctional,” said Habersham, chief electrical officer for MTA New York City Transit's subway system. “Just a simple cleanup won't suffice. We actually have to reconstruct and replace all of this equipment.”

Sandy damaged the New York City subway worse than anything else in its 108-year history, flooding eight tunnels and shutting service for millions of commuters. Recovery efforts began even before the storm was over, and extraordinary work by New York City Transit brought lines back into service rapidly.

Yet while the subway seems back to normal for most of the 5.6 million daily riders, the damage behind the scenes remains extensive – nowhere more so than in the South Ferry electrical room.

Habersham opened the door of an electronics cabinet and pointed to rust stains on a row of programmable logic controllers, which handled signals and switches from South Ferry to the Rector Street station on the 1 train. All of them were ruined.

“This is like taking your computer and just dipping it in salt water,” he said, demonstrating how a bank of switches had failed. “These should snap up and down really easily. The contacts inside are a total loss.”

In front of him stretched banks of wires and electrical contacts that once held hundreds of relays – critical electric components that deliver signal information, control switches and keep trains properly spaced from each other.

Soon after South Ferry was pumped out and drained, crews removed hundreds of relays and tried cleaning them by hand to return them to service – a task that turned out to be futile, as seen by heavy corrosion marks visible on the banks of relays.

“Once you’ve been exposed to that level of salt water, it comes right back,” Habersham said.

Throughout the subway system, metal components that had been inundated by seawater began to corrode and never stopped. Even parts that still function will have a diminished lifespan.

“We reached out to the manufacturers and said, ‘Look, can we salvage this?’ ” Habersham said. “They told us, ‘No, just throw it away. There’s nothing you can do.’ ”

The South Ferry station, built with $545 million in post-9/11 recovery funds, opened in 2009 as a state-of-the-art marvel. It could handle 24 trains an hour on two parallel tracks – a vast improvement over the old station, which could accommodate only half of a 10-car train on a severely curved platform – and was excavated out of bedrock below the existing tangle of Lower Manhattan infrastructure.

Then came Sandy. Though MTA crews tried to barricade the station entrances and ventilation grates before the storm, chest-high water poured down the stairs and filled the station 80 feet deep, from track level to the mezzanine. The rebuilding effort will take an estimated $600 million and as long as three years, and engineers are studying whether some of the vital electrical infrastructure can be moved to higher ground to guard against future flooding.

Not everything can be moved, however: Habersham stepped out of the signal room into the north end of the station, where switches connect the station’s two tracks to each other so trains can enter and leave from either side of the center platform. The switch motors, full of electrical components, were destroyed – and new ones cost $35,000 each.

“In all likelihood,” Habersham said, “this whole machine comes out, and a new one comes in.”